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* <strike>[http://emboss.sourceforge.net/ EMBOSS] - Hundreds of useful, well documented applications for molecular sequence and other analyses.</strike>
* <strike>[http://emboss.sourceforge.net/ EMBOSS] - Hundreds of useful, well documented applications for molecular sequence and other analyses.</strike>
* [http://hannonlab.cshl.edu/fastx_toolkit/index.html FASTX-Toolkit] - Command line tools for Short-Reads FASTA/FASTQ files preprocessing
* [http://hannonlab.cshl.edu/fastx_toolkit/index.html FASTX-Toolkit] - Command line tools for Short-Reads FASTA/FASTQ files preprocessing
* [https://sourceforge.net/projects/gentle-m/ GENtle] - DNA restriction analysis and cloning tool similar to VectorNTI
* [http://www.chevreux.org/projects_mira.html MIRA] - Genome fragment assembler for sequencing projects classified as 'hard' due to high number of similar repeats.
* [http://www.chevreux.org/projects_mira.html MIRA] - Genome fragment assembler for sequencing projects classified as 'hard' due to high number of similar repeats.
* [ftp://ftp.ncbi.nih.gov/toolbox/ NCBI-BLAST and other tools]  - The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences.
* [ftp://ftp.ncbi.nih.gov/toolbox/ NCBI BLAST and other tools]  - The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences.
* [http://www.ncbi.nlm.nih.gov/IEB/ToolBox/SDKDOCS/INDEX.HTML NCBI C Toolkit ] - NCBI libraries and tools for biology applications [http://www.environnement.ens.fr/perso/dumas/fc-srpms/ncbi-6.1.20081116a-1.fc10.src.rpm srpm here]
* [http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/ NCBI C++ Toolkit ] - a new generation of NCBI libraries and tools for biology
* [https://sourceforge.net/projects/pyqpcr/ pyQPCR] - qPCR analysis tool
* <strike>[http://samtools.sourceforge.net/ SAMtools] - SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. Tools for sorting, merging etc. sam format files.</strike>
* <strike>[http://samtools.sourceforge.net/ SAMtools] - SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. Tools for sorting, merging etc. sam format files.</strike>
* [http://staden.sourceforge.net/ Staden]  - sequence handling and analysis software developed at the Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
* [http://staden.sourceforge.net/ Staden]  - sequence handling and analysis software developed at the Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
* [http://www.mygrid.org.uk/tools/taverna/ Taverna] - Tool for automation of experimental workflows.
* [http://www.mygrid.org.uk/tools/taverna/ Taverna] - Tool for automation of experimental workflows.
* [http://www.ncbi.nlm.nih.gov/IEB/ToolBox/SDKDOCS/INDEX.HTML NCBI C Toolkit ] - NCBI libraries and tools for biology applications [http://www.environnement.ens.fr/perso/dumas/fc-srpms/ncbi-6.1.20081116a-1.fc10.src.rpm srpm here]
* [http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/ NCBI C++ Toolkit ] - a new generation of NCBI libraries and tools for biology
* [https://sourceforge.net/projects/gentle-m/ GENtle] - DNA restriction analysis and cloning tool similar to VectorNTI
* [https://sourceforge.net/projects/pyqpcr/ pyQPCR] - qPCR analysis tool


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Revision as of 12:21, 26 May 2010

  • bwa - Burrows-Wheeler Alignment Tool for efficient short read alignment
  • Cytoscape - Platform for the analysis and visualization of complex networks, in particular molecular interaction networks and biological pathways
  • EMBOSS - Hundreds of useful, well documented applications for molecular sequence and other analyses.
  • FASTX-Toolkit - Command line tools for Short-Reads FASTA/FASTQ files preprocessing
  • GENtle - DNA restriction analysis and cloning tool similar to VectorNTI
  • MIRA - Genome fragment assembler for sequencing projects classified as 'hard' due to high number of similar repeats.
  • NCBI BLAST and other tools - The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences.
  • NCBI C Toolkit - NCBI libraries and tools for biology applications srpm here
  • NCBI C++ Toolkit - a new generation of NCBI libraries and tools for biology
  • pyQPCR - qPCR analysis tool
  • SAMtools - SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. Tools for sorting, merging etc. sam format files.
  • Staden - sequence handling and analysis software developed at the Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
  • Taverna - Tool for automation of experimental workflows.
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